A historical and critical analysis of the concept of the gene that attempts to provide new perspectives and metaphors for the transformation of biology and its philosophy.

The concept of the gene has been the central organizing theme of 20th century biology. Biology has become increasingly influential both for philosophers seeking a naturalized basis for epistemology, ethics, and the understanding of the mind, as well as for the human sciences generally. The central task of this work is to get the story right about genes and in so doing provide a critical and enabling resourse for use in the further pursuit of human self-understanding. ;The work begins (...) with a wide-ranging historical reconstruction and conceptual analysis of the meaning of "the gene" that results in defining and distinguishing two different "genes". Each of these can be seen as an heir to one of the two major historical trends in explaining the source of biological order---preformationism and epigenesis. The preformationist gene predicts phenotypes but only on an instrumental basis where immediate medical and/or economic benefits can be had. The gene of epigenesis , by contrast, is a developmental resource that provides templates for RNA and protein synthesis but has in itself no determinate relationship to organismal phenotypes. The seemingly prevalent idea that genes constitute information for traits is based, I argue, upon an unwarranted conflation of these two senses which is in effect held together by rhetorical glue. Beyond this historical, conceptual, and rhetorical inquiry the bulk of the dissertation then concerns itself with an empirically up-to-date analysis of the cell and molecular basis of biological order and of the pathological loss of same. In each of these chapters I structure my analysis with the idea in mind that the "conflated" view can be held empirically accountable. Major touchpoints in this work include the ideas of I. Kant, J. Blumenbach, K. E. von Baer, J. Muller, R. Virchow, W. Johannsen, R. Falk, J. Sapp, E. Schrodinger, M. Delbruick, G. Gamow, R. Doyle, L. Kay, S. Kauffman, E. Jablonka, J. Rothman, K. Yamamoto, P. Rous, H. Temin, J. M. Bishop, H. Harris, E. Stanbridge, D. L. Smithers, B. Vogelstein, E. Farber and H. Rubin. (shrink)

Abstract: Many believe that, in addition to cognitive capacities, autonomous robots need something similar to affect. As in humans, affect, including specific emotions, would filter robot experience based on a set of goals, values, and interests. This narrows behavioral options and avoids combinatorial explosion or regress problems that challenge purely cognitive assessments in a continuously changing experiential field. Adding human-like affect to robots is not straightforward, however. Affect in organisms is an aspect of evolved biological systems, from the taxes of (...) single-cell organisms to the instincts, drives, feelings, moods, and emotions that focus human behavior through the mediation of hormones, pheromones, neurotransmitters, the autonomic nervous system, and key brain structures. We argue that human intelligence is intimately linked to biological affective systems and to the unique repertoire of potential behaviors, sometimes conflicting, they facilitate. Artificial affect is affect in name only and without genes and biological bodies, autonomous robots will lack the goals, interests, and value systems associated with human intelligence. We will take advantage of their general intelligence and expertise, but robots will not enter our intellectual world or apply for legal status in the community. -/- . (shrink)

If the question ``What is a gene?'' proves to be worth asking it must be able to elicit an answer which both recognizes and address the reasons why the concept of the gene ever seemed to be something worth getting excited about in the first place as well analyzing and evaluating the latest develops in the molecular biology of DNA. Each of the preceding papers fails to do one of these and sufferrs the consequences. Where Rolston responds to (...) the apparent failure of molecular biology to make good on the desideratum of the classical gene by veering off into fanciful talk about ``cybernetic genes,'' Griffiths and Stotz lose themselves in the molecular fine print and forget to ask themselves why ``genes'' should be of any special interst anyway. (shrink)

In her recent book Lindley Darden has endeavored to reclaim for philosophy an active role in the elaboration of good science. She has done this, not by holding up some set of rational standards derived from outside of scientific practice, but rather by delving into the history of science and coming out with a set of scientific strategies. Unconcerned about whether any particular strategy wasin fact employed in a given historical case her project depends upon two claims, first that these (...) strategiescould have been successfully deployed in the particular cases from which they were construed, and second and more importantly, that these strategies can be generalized beyond any particular context and be put to future use. It will be argued that Darden''s conception of the possible context independence of scientific strategies is based upon an overly cognitivist misconstrual. An alternative account of the relationship of context dependent and context independent aspects of scientific theory formation will be offered as well as its implications for philosophy. (shrink)

Radically new or unexpected findings in a science demand an openness to new concepts and styles of explanation. The time is more than ripe for asking ourselves what we have learned from the research program of comparative genomics. Where not long ago the human genome was expected to reveal a close association of complexity with the quantitative expansion of the roster of unique genes, more recent findings, especially in relation to comparisons between human and chimp, have raised the bracing possibility (...) that when it comes to complexity, it may be that `less is more'. But `less is more' is not the only observation or inference that follows from the data. The idea of `progressive detachment' will be introduced and set forth as the most perspicuous conceptual resource for unifying and interpreting the overall findings from comparative genomics to date. (shrink)

Vaccinia virus, the world's oldest vaccine, was used originally for the eradication of smallpox. It is now being genetically engineered to create new live vaccines for use against other infectious agents of medical and veterinary importance. Genes coding for antigens of several pathogens have been linked to vaccinia virus transcriptional regulatory signals and inserted into the vaccinia virus genome. The resultant recombinant viruses are infectious, express the foreign gene, stimulate specific immune responses in vaccinated animals and can protect against (...) disease caused by the corresponding pathogen. (shrink)

The essays in this book discuss human behavior and the institutions of capitalism. The essays are non-technical and are written so as to be accessible to students of all disciplines and to all other persons interested in capitalism and in economic behavior. They often present unconventional views of the topics they discuss. Those containing unconventional views discuss self-interested behavior, selfish gene theory, the meaning and social function of private ownership, the externality problem, the nature of the firm and the (...) rise of capitalism. The essays are not meant to be a textbook, but they offer a useful supplementary reading source for courses in business, economics and law that deal with human behavior in the marketplace and with capitalism, ownership, markets and firms. (shrink)

Recognition of the plasticity of development — from gene expression to neuroplasticity — is increasingly undermining the traditional distinction between structure and function, or anatomy and behavior. At the same time, dynamic systems theory — a set of tools and concepts drawn from the physical sciences — has emerged as a way of describing what Maurice Merleau-Ponty calls the “dynamic anatomy” of the living organism. This article surveys and synthesizes dynamic systems models of development from biology, neuroscience, and psychology (...) in order to propose an integrated account of growth, learning, and behavior. Key to this account is the concept of self-differentiation or symmetry-breaking. I argue that development can be understood as a cascade of symmetry-breaking events brought about by the ongoing interactions of multiple, nested, nonlinear dynamic systems whose self-organizing behaviors gradually alter their own anatomical conditions. I begin by introducing the concept of symmetry-breaking as a way of understanding anatomical development. I then extend this approach to motor development by arguing that the organism’s behavior grows along with its body, like a new organ. Finally, I argue that the organism’s behavior and its world grow together dialectically, each driving the other to become more complex and asymmetrical through its own increasing asymmetry. Thus development turns out to be a form of cognition or sense-making, and cognition a form of development. (shrink)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

Book review of Lenny Moss, What Genes Can’t Do. Cambridge, MA: MIT Press , 256 pp. -/- Many philosophers of science will have encountered the core distinction between two different gene concepts found in What Genes Can’t Do. Moss argues that contemporary uses of the term ‘gene’ that denote an information bearing entity result from the conflation of two concepts (‘Gene-P’ and ‘Gene-D’).

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO (...) relates to UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a (...) framework for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (shrink)

Philosophy of Science, 73 (April 2006) pp. 247–257. 0031-8248/2006/7302-0007$10.00 Copyright 2006 by the Philosophy of Science Association. All rights reserved. 247 BOOK REVIEWS Lenny Moss, What Genes Can’t Do . Cambridge, MA: MIT Press (2004), 256 pp., $21.00 (paper). Many philosophers of science will have encountered the core distinction between two different gene concepts found in What Genes Can’t Do . Moss argues that contemporary uses of the term ‘gene’ that denote an infor- mation bearing entity (...) result from the conflation of two concepts (‘Gene- P’ and ‘Gene-D’). These concepts arise out of distinct trajectories in the history of biology (preformation and epigenesis, respectively) but are glued together by the rhetoric of linguistic and textual metaphors (e.g., blueprints and programs). Gene-P picks out an instrumentalist use of ‘gene’ as phenotypic indicator or predictor, whereas Gene-D refers to DNA sequences as developmental template resources for RNA and pro- tein products that play variegated cellular roles in the production of many, distinct phenotypes. A number of critical responses to the distinction are now extant in the literature, but my aim is to answer a different question. Why should philosophers of science who have not read the book be interested in it (besides the fact that it is now available in paperback)? The answer is found at the level of methodology and is relevant to crit- icisms of Moss’s distinction. (shrink)

This article examines how minimal genome research mobilizes philosophical concepts such as minimality and essentiality. Following a historical approach the article aims to uncover what function this terminology plays and which problems are raised by them. Specifically, four historical moments are examined, linked to the work of Harold J. Morowitz, Mitsuhiro Itaya, Eugene Koonin and Arcady Mushegian, and J. Craig Venter. What this survey shows is a historical shift away from historical questions about life or descriptive questions about specific (...) organisms towards questions that explore biological possibilities: what are possible forms of minimal genomes, regardless of whether they exist in nature? Moreover, it highlights a fundamental ambiguity at work in minimal genome research between a universality claim and a standardization claim: does a minimal genome refer to the minimal gene set for any organism whatsoever? Or does it refer rather to a gene set that will provide stable, robust and predictable behaviour, suited for biotechnological applications? Two diagnoses are proposed for this ambiguity: a philosophical diagnosis of how minimal genome research either misunderstands the ontology of biological entities or philosophically misarticulates scientific practice. Secondly, a historical diagnosis that suggests that this ambiguity is part of a broader shift towards technoscience. (shrink)

In March 1996, the General Accounting Office (GAO) issued the reportScientific Research: Continued Vigilance Critical to Protecting Human Subjects.It stated that “an inherent conflict of interest exists when physician-researchers include their patients in research protocols. If the physicians do not clearly distinguish between research and treatment in their attempt to inform subjects, the possible benefits of a study can be overemphasized and the risks minimized.” The report also acknowledged that “the line between research and treatment is not always cleartoclinicians. Controversy (...) exists regarding whether certain medical procedures should be categorized as research.”This problem currently plagues gene transfer research. A few months prior to the GAO report, an ad hoc committee appointed by National Institutes of Health (NIH) Director Harold Varmus expressed similar concerns in its assessment of NIH investment in research on gene therapy. (shrink)

Book Review: What Genes Can’t Do By Lenny Moss .

In March 1996, the General Accounting Office (GAO) issued the reportScientific Research: Continued Vigilance Critical to Protecting Human Subjects.It stated that “an inherent conflict of interest exists when physician-researchers include their patients in research protocols. If the physicians do not clearly distinguish between research and treatment in their attempt to inform subjects, the possible benefits of a study can be overemphasized and the risks minimized.” The report also acknowledged that “the line between research and treatment is not always cleartoclinicians. Controversy (...) exists regarding whether certain medical procedures should be categorized as research.”This problem currently plagues gene transfer research. A few months prior to the GAO report, an ad hoc committee appointed by National Institutes of Health (NIH) Director Harold Varmus expressed similar concerns in its assessment of NIH investment in research on gene therapy. (shrink)

In March 1996, the General Accounting Office issued the report Scientific Research: Continued Vigilance Critical to Protecting Human Subjects. It stated that “an inherent conflict of interest exists when physician-researchers include their patients in research protocols. If the physicians do not clearly distinguish between research and treatment in their attempt to inform subjects, the possible benefits of a study can be overemphasized and the risks minimized.” The report also acknowledged that “the line between research and treatment is not always clear (...) to clinicians. Controversy exists regarding whether certain medical procedures should be categorized as research.”This problem currently plagues gene transfer research. A few months prior to the GAO report, an ad hoc committee appointed by National Institutes of Health Director Harold Varmus expressed similar concerns in its assessment of NIH investment in research on gene therapy. (shrink)

" --Maurice A. Finocchiaro,Isis "The best and most original aspect of the book is its overall conception.

This experimental study evaluated the influence of stated organizational concern for ethical conduct upon managerial behavior. Using an in-basket to house the manipulation, a sample of 113 MBA students with some managerial experience reacted to scenarios suggesting illegal conduct and others suggesting only unethical behavior. Stated organizational concern for ethical conduct was varied from none (control group) to several other situations which included a high treatment consisting of a Code of Ethics, an endorsement letter by the CEO and specific sanctions (...) for managerial misconduct. Only in the case of suggested illegal behavior tempered by high organizational concern were managers influenced by organizational policy to modify the morality of their actions. However, the responses to the illegal scenarios were significantly more ethical than the reactions given to the unethical (but not illegal) situations. The implications of these findings are then discussed. (shrink)

Thrasyllus, best known as the Roman emperor Tiberius' astrologist, figured prominently in the development of ancient Platonism. How prominently and to what effect are questions that have puzzled philosophers down to our day; Harold Tarrant's important new book attempts to answer them.

What grounds a judgment that a work of art is immoral? This book argues that we cannot judge artworks morally in the same way that we judge people. What>'s more, there is no direct influence from moral judgments to aesthetic judgments: it is possible for artworks to be both immoral and beautiful.

In this book, Eli Hirsch focuses on identity through time, first with respect to ordinary bodies, then underlying matter, and eventually persons. These are linked at various points with other aspects of identity, such as the spatial unity of things, the unity of kinds, and the unity of groups. He investigates how our identity concept ordinarily operates in these respects. He also asks why this concept is so cental to our thinking and whether we can justify seeing the world in (...) terms of such a concept. This is the revised and updated edition of a hardback published in 1982. (shrink)

In the first twelve chapters of this book, I am concerned with the Fregean notion of an object (the reference of a proper name) and its connection with the notion of identity. The rest of the book is devoted to a discussion of the problem of personal identity.

The aim of the paper is to discuss some recent variants of familiar puzzles concerning the relations of parts to wholes put forward by Trenton Merricks and Eric Olson. The argument is put forward that so long as the familiar distinction between 'loose and popular' and 'strict and philosophical' senses of identity claims is accepted the paradoxical conclusions at which Merricks and Olson arrive can be resisted. It is not denied that accepting the distinction between 'loose and popular' and 'strict (...) and philosophical' senses of identity claims is itself a departure from common-sense, but it is argued that it is the smallest such departure available to us. (shrink)

Since the introduction of the U.S. Sarbanes-Oxley Act in 2002 and several other national corporate governance codes, whistleblowing policies have been implemented in a growing number of companies. Existing research indicates that this type of governance codes has a limited direct effect on ethical or whistleblowing behaviour whereas whistleblowing policies at the corporate level seem to be more effective. Therefore, evidence on the impact of (inter)national corporate governance codes on the content of corporate whistleblowing policies is important to understand their (...) indirect impact on whistleblowing behaviour. This study analyzes the contents of whistleblowing policies, and parts of corporate codes of conduct and codes of ethics, describing such policies of 56 leading European companies. By classifying the contents in seven categories, an exploratory framework was created. General contents often identified were: applicability to all employees, a group-wide scope and an authoritative tone. The most common general violations to report were breaches of internal policies and external regulations or laws. The more specific violations most frequently mentioned were criminal offences and dangers to health and safety or the environment. Contacts to report to were the direct or indirect supervisors, a compliance officer or a confidential “hotline” facility. A confidentiality guarantee was common and anonymous reporting was often possible, though sometimes discouraged. Protection against retaliation is stated by ensuring that retaliation will not happen, prohibiting it or making it punishable. The requirement of good faith was frequently given. Finally, investigation of the report was often guaranteed. Surprisingly little information is given on the treatment of whistleblowers reporting an unfounded complaint in good faith, or reporting a violation they were involved in. The study’s findings are most relevant to companies without a whistleblowing policy or those that intend to benchmark their policies, and to pan-European standard setters. (shrink)

Recent work by Jaegwon Kim and others suggest that functionalism leaves mental properties causally inefficacious in some sense. I examine three lines of argument for this conclusion. The first appeals to Occam's Razor; the second appeals to a ban on overdetermination; and the third charges that the kind of response I favor to these arguments forces me to give up "the homogeneity of mental and physical causation". I show how each argument fails. While I concede that a positive theory of (...) mental causation is desirable, there is no reason to think that functionalism renders such a theory unattainable. (shrink)